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Yorodumi- PDB-6oti: Carbonic Anhydrase IX mimic complexed with ureic benzene sulfonam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oti | ||||||
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Title | Carbonic Anhydrase IX mimic complexed with ureic benzene sulfonamide MB9-561B | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | lyase/lyase inhibitor / ureido benzene sulfonamide / carbonic anhydrase / inhibitor / LYASE / lyase-lyase inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kota, A. / McKenna, R. | ||||||
Citation | Journal: To Be Published Title: Carbonic Anhydrase IX mimic complexed with ureido benzene sulfonamide MB9-561B Authors: Kota, A. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oti.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oti.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 6oti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oti_validation.pdf.gz | 740.1 KB | Display | wwPDB validaton report |
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Full document | 6oti_full_validation.pdf.gz | 741.1 KB | Display | |
Data in XML | 6oti_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6oti_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/6oti ftp://data.pdbj.org/pub/pdb/validation_reports/ot/6oti | HTTPS FTP |
-Related structure data
Related structure data | 6otkC 6otmC 6otpC 6oufC 3ks3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28844.465 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-N84 / |
#4: Chemical | ChemComp-TRS / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M Sodium Citrate, 50mM Tris-HCL, pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryo / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.86 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.323 Å / Num. obs: 16030 / % possible obs: 94.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 20.71 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.64 |
Reflection shell | Resolution: 2→2.072 Å / Rmerge(I) obs: 0.33 / Num. unique obs: 1625 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 2→29.323 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.41 Å2 / Biso mean: 27.3923 Å2 / Biso min: 4.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→29.323 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: -30.4337 Å / Origin y: -1.3699 Å / Origin z: 16.1508 Å
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Refinement TLS group |
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